Start up functions

Read and organize data

read_srm_export <- function(filename, columns = c("peak_name", "RT.min", "basepeak", "area.cpm", "height.cts", "quantitation")) {
  filename %>% 
    # read excel files
    read_excel(sheet = "Integration", skip = 42, 
               col_names = columns, col_types = rep("text", length(columns))) %>% 
    as_data_frame() %>%
    # remove empty rows
    filter(!is.na(peak_name), peak_name != "n.a.") %>% 
    # convert the relevant numeric columns into numbers
    mutate_at(vars(RT.min, area.cpm, height.cts), as.numeric) %>% 
    # remove useless columns
    select(-basepeak, -quantitation) %>% 
    # add filename info
    mutate(file_id = gsub("\\.xls", "", basename(filename))) %>% 
    select(file_id, everything())
}

# get data
all_data <- 
  # find all excel files ##change name and use new folder for new project
  list.files("data_SH1", recursive = TRUE, full.names = TRUE, pattern = "\\.xls$") %>% 
  # send them to the read method
  lapply(read_srm_export) %>% 
  # combine the data set
  bind_rows() %>% 
  # pull out sample information
  #mutate(sample_id = str_match(all_data$file_id, "TSQ\\d+_GB_(.*)$") %>% { .[,2] }) %>% 
  # get n replicates
  group_by(file_id)
  #mutate(n_replicates = length(unique(file_id)))

File names for metadata file

Plot to check the spread

by sequence

all_data %>% 
  ggplot() + 
  aes(x = peak_name, y = area.cpm, color = file_id) +
  geom_point(size = 3) +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))

##by sample

all_data %>% 
  ggplot() +
  aes(x = file_id, y = area.cpm, color = file_id) + 
  geom_point(size = 3) +
  facet_wrap(~peak_name, scales = "free_y") +
    theme_bw() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
        legend.position = "none")

Calculation peak amounts and rock concentrations, ID standards

depth_and_rock_info <- read_excel(file.path("metadata", "aliphaticSRM_SH1.xlsx")) %>% 
  rename(tle = `TLE.mg`, maltene = `maltenes.mg`, ref_amount_added.ug = `D4.ug` )%>% 
  filter(!is.na(file_id))
kable(depth_and_rock_info)
file_id OG depth rock.g tle maltene ref_amount_added.ug process
TSQ3481_GB_OG002 2 125.015 10.001 24.9 13.7 100 yes
TSQ3482_GB_OG003 3 124.000 10.120 224.4 7.3 100 yes
TSQ3483_GB_OG004 4 123.000 10.320 -14.4 5.0 100 yes
TSQ3484_GB_OG005 (50_) 5 122.000 9.280 3.2 5.4 100 yes
TSQ3485_GB_OG006 6 121.000 10.624 33.4 NA 100 yes
TSQ3486_GB_OG007 7 119.000 9.620 -214.2 4.8 100 yes
TSQ3489_GB_OG008 8 118.000 9.698 3.4 5.0 100 yes
TSQ3490_GB_OG009 9 117.010 10.742 5.0 6.3 100 yes
TSQ3491_GB_OG010 10 115.000 11.070 5.0 6.0 100 yes
TSQ3492_GB_OG011 11 114.000 10.208 0.4 6.9 100 yes
TSQ3495_GB_OG012 12 113.000 10.552 9.4 11.4 100 yes
TSQ3496_GB_OG013 13 111.080 9.747 6.9 9.5 100 yes
TSQ3497_GB_OG014 (25_) 14 110.100 10.273 14.5 14.0 100 yes
TSQ3498_GB_OG015 15 109.100 10.984 13.3 15.3 100 yes
TSQ3477_GB_OG016 16 108.300 10.089 5.1 NA 100 no
TSQ3499_GB_OG017 17 106.900 10.348 -6.2 6.8 100 yes
TSQ3476_GB_OG018 18 106.090 10.337 4.9 6.5 100 yes
TSQ3473_GB_OG019 19 105.100 11.002 2.2 -5.2 100 yes
TSQ3474_GB_OG020 20 104.090 10.911 5.6 7.2 100 yes
TSQ3475_GB_OG021 21 102.890 10.056 21.6 7.4 100 yes
TSQ3466_GB_OG022 22 101.900 11.025 4.5 7.2 100 yes
TSQ3467_GB_OG023 23 101.100 11.294 8.5 NA 100 yes
TSQ3468_GB_OG025 25 98.900 10.713 7.8 8.6 100 yes
TSQ3469_GB_OG026 26 98.090 9.336 4.7 7.4 100 yes
TSQ3472_GB_OG027 27 96.890 9.378 5.3 6.3 100 yes
TSQ3503_GB_OG028 28 96.090 9.758 6.9 7.3 100 yes
TSQ3504_GB_OG029 29 95.080 11.469 4.3 2.3 100 yes
TSQ3505_GB_OG030 30 94.560 10.195 7.1 8.2 100 yes
TSQ3506_GB_OG031 31 119.950 7.502 2.6 4.7 100 yes
TSQ3507_GB_OG032 32 115.885 9.032 -2.1 4.4 100 yes
TSQ3508_GB_OG033 33 112.070 7.287 2.3 -7.2 100 yes
TSQ3511_GB_OG037 37 121.600 10.534 5.2 3.6 100 yes
TSQ3512_GB_OG038 38 120.700 11.444 3.3 2.2 100 yes
TSQ3513_GB_OG039 39 120.100 7.997 0.8 0.9 100 yes
TSQ3514_GB_OG041 41 120.405 11.393 2.3 1.9 100 yes
TSQ3515_GB_OG042 42 120.205 10.757 NA NA 100 yes
TSQ3516_GB_OG043 43 122.900 11.349 14.7 11.9 100 yes
TSQ3519_GB_OG044 44 120.300 11.390 3.5 2.7 100 yes
TSQ3520_GB_OG045 45 120.205 10.757 4.1 2.4 100 yes
TSQ3521_GB_OG046 46 121.500 11.191 24.7 3.1 100 yes
TSQ3522_GB_OG047 (50_) 47 121.105 10.868 38.8 5.5 100 yes
TSQ3523_GB_OG049 49 122.600 11.260 30.0 12.7 100 yes
TSQ3524_GB_OG050 (50_) 50 120.600 11.195 16.1 2.1 100 yes
TSQ3527_GB_OG051 51 120.900 14.166 96.8 6.3 100 yes
TSQ3528_GB_OG052 52 121.800 10.268 4.5 3.0 100 yes
TSQ3529_GB_OG053 53 122.805 10.786 71.2 6.7 100 yes
TSQ3530_GB_OG054 54 122.700 12.054 77.3 13.5 100 yes
TSQ3531_GB_OG056 56 121.700 11.024 22.8 3.0 100 yes
TSQ3532_GB_OG057 57 122.500 10.939 36.8 12.6 100 yes
TSQ3535_GB_OG058 58 121.195 10.711 18.4 4.2 100 yes
TSQ3536_GB_OG059 59 122.090 9.486 54.9 3.6 100 yes
TSQ3537_GB_OG060 60 122.200 11.367 53.3 2.8 100 yes
TSQ3538_GB_OG061 61 121.400 12.044 40.7 4.0 100 yes
TSQ3539_GB_OG062 62 120.950 10.341 83.1 7.8 100 yes
TSQ3540_GB_OG063 63 122.390 10.116 139.5 8.8 100 yes
TSQ3541_GB_OG064 64 122.305 10.957 42.9 2.2 100 yes
TSQ3544_GB_OG065 65 107.900 10.694 40.0 5.3 100 yes
TSQ3634_GB_OG153 153 116.810 11.177 9.8 3.9 100 yes
TSQ3635_GB_OG154 154 116.600 12.080 29.1 3.6 100 yes
TSQ3636_GB_OG155 155 119.850 11.042 7.1 1.6 100 yes
TSQ3637_GB_OG156 156 117.400 11.244 8.0 3.3 100 yes
TSQ3638_GB_OG157 157 118.800 11.346 8.3 2.6 100 yes
TSQ3639_GB_OG158 158 119.550 11.853 7.6 3.2 100 yes
TSQ3647_GB_OG159 159 119.655 11.044 6.7 3.8 100 yes
TSQ3648_GB_OG160 160 118.300 11.305 7.4 2.1 100 yes
TSQ3649_GB_OG161 161 116.490 10.770 8.4 2.9 100 yes
TSQ3650_GB_OG162 162 116.900 10.931 10.9 4.1 100 yes
TSQ3654_GB_OG164 164 118.100 10.619 7.6 3.5 100 yes
TSQ3655_GB_OG165 165 119.570 11.300 5.0 1.6 100 yes
TSQ3656_GB_OG166 166 118.600 10.790 7.1 1.9 100 yes
TSQ3657_GB_OG167 167 117.490 10.853 8.8 2.9 100 yes
TSQ3658_GB_OG168 168 118.965 11.259 6.3 2.0 100 yes 
data_by_depth <- 
  all_data %>%
  left_join(depth_and_rock_info, by = "file_id") %>% 
  group_by(file_id) %>% 
  mutate(
    n_peaks = n(),
    n_standards = sum(peak_name == "D4 C29 ISTD"),
    ref_area.cpm = area.cpm[peak_name == "D4 C29 ISTD"],
    amount.ug = area.cpm/ref_area.cpm * ref_amount_added.ug,
   
    #Normalize by what you want
    conc_rock.ug_g = amount.ug / rock.g, 
    conc_tle.ug.g = amount.ug / tle,  
    conc_maltene.ug.g = amount.ug / maltene
    
  )%>% ungroup() %>% 
  arrange(file_id, peak_name) 

data_by_depth

Calculate Recovery

Linear regressions of the calibration curves

standard <- read_excel(file.path("metadata", "D4_calibration.xlsx"))   ###read excel

###calibration curve
standard %>% 
  ggplot() +
  aes(x = Known.ng, y = Measured_area.counts, color = calibration) + 
  geom_smooth(method = "lm", alpha = 0.5) +
  geom_point() +
  theme_bw() +
  theme(legend.position = "none") 

calibrations <- 
  standard %>% 
  filter(!is.na(calibration)) %>% 
  nest(-calibration) %>% 
  mutate(
    fit = map(data, ~summary(lm(`Measured_area.counts`~ `Known.ng`, data = .x))),
    coefficients = map(fit, "coefficients"),
    intercept = map_dbl(coefficients, `[`, 1, 1),
    intercept_se = map_dbl(coefficients, `[`, 1, 2),
    slope = map_dbl(coefficients, `[`, 2, 1),
    slope_se = map_dbl(coefficients, `[`, 2, 2),
    r2 = map_dbl(fit, "r.squared")
  )

calibrations %>% select(-data, -fit, -coefficients) %>% knitr::kable(d = 3)
calibration intercept intercept_se slope slope_se r2
jan2018 705.862 1371.146 72929.67 3337.256 0.996

Determine yield

These numbers are not useful for anything else.

calib_data <-
  data_by_depth %>% 
  # temp
  mutate(calibration = "jan2018") %>% 
  left_join(calibrations, by = "calibration") %>% 
  mutate(
    total_volume.uL = 100,
    total_inject.uL = 1.5,
    ref_amount_inject_expected.ng = (ref_amount_added.ug * 1000)/total_volume.uL * total_inject.uL ,
    ref_amount_inject_measured.ng = (ref_area.cpm - intercept)/slope,
    ref_amount_measured.ug = ((total_volume.uL* ref_amount_inject_measured.ng)/total_inject.uL) * 1/1000,
    yield = (ref_amount_inject_measured.ng/ref_amount_inject_expected.ng) * 100
  )
  
calib_data

check yields

calib_data %>% 
  select(file_id, peak_name, yield)  %>% 
  arrange(file_id)  %>% 
  unique() %>% 
  ggplot() + aes(file_id, y = yield) +
  geom_point(size = 3) +
  theme_bw() + theme(axis.text.x = element_text(angle = 90, hjust = 0, vjust = 0.5))
## Warning: Removed 1938 rows containing missing values (geom_point).

Combine compounds/make ratios (new rows w/o RTs etc, just concentration.rock column)

# functions to make it easy to sum up peaks

sum_peaks <- function(df, filter_condition, new_peak_name) {
  filter_condition <- sprintf("(%s)", str_c(filter_condition, collapse = "|"))
  filter(df, str_detect(peak_name, filter_condition)) %>% 
    summarize(
      file_id = file_id[1],
      depth = depth[1],
      conc_rock.ug_g = sum(conc_rock.ug_g)
    ) %>% 
    mutate(peak_name = new_peak_name)
}

ratio_peaks <- function(df, filter_top, filter_bottom, new_peak_name) {
  filter_top <- sprintf("(%s)", str_c(filter_top, collapse = "|"))
  filter_bottom <- sprintf("(%s)", str_c(filter_bottom, collapse = "|"))
  filter(df, str_detect(peak_name, filter_top) | str_detect(peak_name, filter_bottom)) %>% 
    summarize(
      file_id = file_id[1],
      depth = depth[1],
      ratio = sum(conc_rock.ug_g[str_detect(peak_name, filter_top)]) / sum(conc_rock.ug_g[str_detect(peak_name, filter_bottom)])
    ) %>% 
    mutate(peak_name = new_peak_name)
}

Ideas for other ratios? What about dimethyls?

#set values to use for later calculations
final_data1 <- calib_data %>% 
    group_by(file_id) %>% 
        do({
          bind_rows(., 
              #C27_Dia/Reg
                sum_peaks(.,  c("C27 aB 20R ST", "C27 aB 20S ST"), "C27Dia"),      
                sum_peaks(., c("C27 aaa 20R ST", "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C27 Ba 20R ST", "C27 Ba 20S ST"), "C27Reg"),
            
              #Total Tricyclics
                sum_peaks(., c("C19 Tri HO", "C20 Tri HO", "C21 Tri HO", "C22 Tri HO", "C23 Tri HO", "C24 Tet HO", "C24 Tri HO", "C25 Tri R HO", "C25 Tri S HO", "C26 Tri R HO", "C26 Tri S HO"), "all_tricyclics"),
            
              #4Me_TriMe
                sum_peaks(., c("4B Me 5a cholestane", "4B Me 24 ethyl 5a cholestane", "4B,23S,24S trimethyl 5a cholestane", "4B,23S,24R trimethyl 5a cholestane", "4B,23R,24S trimethyl 5a cholestane", "4B,23R,24R trimethyl 5a cholestane", "4a Me 5a cholestane", "4a Me 24 ethyl 5a cholestane", "4a,23S,24S trimethyl 5a cholestane", "4a,23S,24R trimethyl 5a cholestane", "4a,23R,24S trimethyl 5a cholestane", "4a,23R,24R trimethyl 5a cholestane"), "4Me_TriMe"),
            
              #allRegSt
                sum_peaks(., c("C26 aBB 20S ST", "C26 aBB 20R ST", "C26 aaa 20S ST", "C26 aaa 20R ST","C27 aBB 20S ST", "C27 aBB 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST","C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aBB 20 R+S ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), "allRegst"),
            
              #allRegHO
                sum_peaks(., c("Ts C27 HO", "Tm C27 HO", "C27 17B H Ho", "29, 30 C28H bisnor HO", "28, 30 C28 bisnor HO", "C29 Ts HO", "C29 Ba HO", "C29 BB Ho", "C30 aB HO", "C30 BB HO", "C30H Ba HO", "C31 HR Ba HO", "C31 aB HR HO", "C31 aB HS HO", "C31 BB HO", "C32 aB HS HO", "C32 aB HR HO", "C33 aB HS HO", "C33 aB HR HO", "C34 aB HR HO", "C34 aB HS HO", "C35 aB HR HO", "C35 aB HS HO"), "allRegHO") 
            
) }) %>% ungroup()
final_data <- final_data1 %>% 
    group_by(file_id) %>% 
        do({
          bind_rows(., 
            #Thermal Maturity
              #C27_Dia/Reg
                ratio_peaks(., "C27Dia", "C27Reg", "C27Dia/Reg"),
              #C27Dia_S/R
                ratio_peaks(., "C27 aB 20R ST", "C27 aB 20S ST", "C27Dia_S/R"),
              #C27Reg_abb/all 
                 ratio_peaks(., c("C27 aBB 20R ST", "C27 aBB 20S ST"), c("C27 aaa 20R ST", "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST"), "C27Reg_abb/aaa"),
              #C27RegaaaS/S+R
                ratio_peaks(., "C27 aaa 20S ST", c("C27 aaa 20R ST", "C27 aaa 20S ST"), "C27Regaaa_S/S+R"), 
              #C27RegabbS/S+R
                ratio_peaks(., "C27 aBB 20S ST", c("C27 aBB 20S ST", "C27 aBB 20R ST"), "C27Regabb_S/S+R"),
              #C28Dia/all
                ratio_peaks(., c("C28 Ba 20S ST", "C28 Ba 20R ST"), c("C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C28 Ba 20S ST", "C28 Ba 20R ST"), "C28Dia/all"),
              #C28DiaS/S+R
                ratio_peaks(., "C28 Ba 20S ST", c("C28 Ba 20S ST", "C28 Ba 20R ST"), "C28DiaS/S+R"),
              #C28abb/all
                ratio_peaks(., c("C28 aBB 20S ST", "C28 aBB 20R ST"), c("C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST"), "C28abb/all"),
              #C28aaaS/S+R
                ratio_peaks(., "C28 aaa 20S ST", c("C28 aaa 20S ST", "C28 aaa 20R ST"), "C28aaaS/S+R"),
              #C28abbS/S+R
                ratio_peaks(., "C28 aBB 20S ST", c("C28 aBB 20S ST", "C28 aBB 20R ST"), "C28abbS/S+R"),
              #C29Dia/all
                ratio_peaks(., c("C29 Ba 20S ST", "C29 Ba 20R ST"),  c("C29 Ba 20S ST", "C29 Ba 20R ST", "C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST"), "C29Dia/all"),
              #C29DiaS/S+R
                ratio_peaks(., "C29 Ba 20S ST", c("C29 Ba 20S ST", "C29 Ba 20R ST"), "C29DiaS/S+R"),
              #C29abb/all
                ratio_peaks(., c("C29 aBB 20S ST", "C29 aBB 20R ST"), c( "C29 aaa 20S ST", "C29 aaa 20R ST", "C29 aBB 20S ST", "C29 aBB 20R ST" ), "C29abb/all"),
              #C29aaaS/S+R
                ratio_peaks(., "C29 aaa 20S ST", c("C29 aaa 20S ST", "C29 aaa 20R ST") , "C29aaaS/S+R"),
              #C29abbS/S+R
                ratio_peaks(., "C29 aBB 20S ST", c("C29 aBB 20S ST", "C29 aBB 20R ST"), "C29abbS/S+R"),
              #C27Ts/Ts+Tm
                ratio_peaks(., "Ts C27 HO", c("Ts C27 HO", "Tm C27 HO"), "C27Ts/Tm"),
              #C28BNH29,30/28,30
                ratio_peaks(., "29, 30 C28 bisnor HO", c("29, 30 C28 bisnor HO", "28, 30 C28 bisnor HO"), "C28BNH29,30/28,30"),
              #C29Ts/Ts+ab
                ratio_peaks(., "C29 Ts HO", c( "C29 aB HO", "C29 Ts HO"), "C29Ts/ab"),
              #C29ba/ba+ab
                ratio_peaks(.,"C29 Ba HO",  c("C29 aB HO", "C29 Ba HO"), "C29ba/ab"),
              #C29bb/bb+ab
                ratio_peaks(., "C29 BB Ho", c("C29 BB Ho", "C29 aB HO"), "C29bb/ab"),
              #C30_30nor/30nor+ab
                ratio_peaks(., "30-nor C30H HO", c("C30 aB HO", "30-nor C30H HO"),  "C30_30nor/ab"),
              #C30ba/ba+ab
                ratio_peaks(., "C30H Ba HO", c("C30 aB HO", "C30H Ba HO"), "C30ba/ab"),
              #C30bb/bb+ab
                ratio_peaks(., "C30 BB HO", c("C30 aB HO", "C30 BB HO"), "C30bb/ab"),
              #C31S/S+R
                ratio_peaks(., "C31 aB HS HO", c("C31 aB HR HO", "C31 aB HS HO"), "C31S/S+R"),
              #C32S/S+R
                ratio_peaks(., "C32 aB HS HO", c("C32 aB HS HO", "C32 aB HR HO"), "C32S/S+R"),
              #C33S/S+R
                ratio_peaks(., "C33 aB HS HO", c("C33 aB HS HO", "C33 aB HR HO"), "C33S/S+R"),
              #C34S/S+R
                ratio_peaks(., "C34 aB HS HO", c("C34 aB HS HO", "C34 aB HR HO") , "C34S/S+R"),
              #C35S/S+R
                ratio_peaks(., "C35 aB HS HO", c("C35 aB HS HO", "C35 aB HR HO") , "C35S/S+R"),
           #Source
              #C19/tricyclics
                ratio_peaks(., "C19 Tri HO", "all_tricyclics", "C19/tricyclics"),
              #C20/tricyclics
                ratio_peaks(., "C20 Tri HO", "all_tricyclics", "C20/tricyclics"),
              #C21/tricyclics
                ratio_peaks(., "C21 Tri HO", "all_tricyclics", "C21/tricyclics"),
              #C22/tricyclics
                ratio_peaks(., "C22 Tri HO", "all_tricyclics", "C22/tricyclics"),
              #C23/tricyclics
                ratio_peaks(., "C23 Tri HO", "all_tricyclics", "C23/tricyclics"),
              #C24/tricyclics
                ratio_peaks(., c("C24 Tet HO", "C24 Tri HO"), "all_tricyclics", "C24/tricyclics"),
              #C25/tricyclics
                ratio_peaks(., c("C25 Tri R HO", "C25 Tri S HO"), "all_tricyclics", "C25/tricyclics"),
              #C26/tricyclics
                ratio_peaks(., c("C26 Tri R HO", "C26 Tri S HO"), "all_tricyclics", "C26/tricyclics"),
              #tricyclics/all
                ratio_peaks(., "all_tricyclics", c(""), "tricyclics/all"),
              #C19/C19+23
                ratio_peaks(., "C19 Tri HO", c("C19 Tri HO", "C23 Tri HO"), "C19/C19+23"),
              #C20/C20+23
                ratio_peaks(., "C20 Tri HO", c("C20 Tri HO", "C23 Tri HO"), "C20/C20+23"),
           
              #C26St/allSt ##INCLUDES ME's
                ratio_peaks(., c("C26 Ba 20S ST", "C26 Ba 20R ST", "C26 aBB 20S ST", "C26 aBB 20R ST", "C26 aaa 20S ST", "C26 aaa 20R ST"), c("cholestane", "ST"), "C26St/allSt"), 
              #C27St/allSt
                ratio_peaks(., c("C27 aaa 20R ST", "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C27 Ba 20R ST", "C27 Ba 20S ST"), c("cholestane", "ST"), "C27St/allSt"),
              #C28St/allSt
                ratio_peaks(., c("C28 Ba 20S ST", "C28 Ba 20R ST", "C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST"), c("cholestane", "ST"), "C28St/allSt"),
              #C29St/allSt
                ratio_peaks(., c("C29 Ba 20S ST", "C29 Ba 20R ST", "C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST"), c("cholestane", "ST"), "C29St/allSt"),
              #C30St/allSt (does not include Me's in numerator)
                ratio_peaks(., c("C30 Ba 20S ST", "C30 Ba 20R ST", "C30 aBB 20(R+S) ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), c("cholestane", "ST"), "C30St/allSt"),
              #C30Me/allSt (C30 Me's in numerator)(not in MRM spreadsheet)
                ratio_peaks(., c("C30 4a Me 20S ST", "C30 4a Me 20R ST + DINO st", "C30 3B Me BB 20S ST", "C30 3B Me BB 20R ST", "C30 3B Me 20S ST", "C30 3BMe 20R ST", "C30 2aMe 20S ST", "C30 2a Me 20R + 4a Me BB 20S ST"), c("cholestane", "ST"), "C30Me/allSt"),
              #DinoSt/allSt
                ratio_peaks(., c("4B Me 5a cholestane", "4B Me 24 ethyl 5a cholestane", "4B,23S,24S trimethyl 5a cholestane", "4B,23S,24R trimethyl 5a cholestane", "4B,23R,24S trimethyl 5a cholestane", "4B,23R,24R trimethyl 5a cholestane", "4a Me 5a cholestane", "4a Me 24 ethyl 5a cholestane", "4a,23S,24S trimethyl 5a cholestane", "4a,23S,24R trimethyl 5a cholestane", "4a,23R,24S trimethyl 5a cholestane", "4a,23R,24R trimethyl 5a cholestane"), c("cholestane", "ST"), "DinoSt/allSt"),
           
              #C26/(C26-30)aaaSR
                ratio_peaks(., c("C26 aaa 20R ST", "C26 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C26/(C26-30)aaaSR"),
              #C27/(C26-30)aaaSR
                ratio_peaks(., c("C27 aaa 20R ST", "C27 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C27/(C26-30)aaaSR"),
              #C28/(C26-30)aaaSR
                ratio_peaks(., c("C28 aaa 20R ST", "C28 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C28/(C26-30)aaaSR"),
              #C29/(C26-30)aaaSR
                ratio_peaks(., c("C29 aaa 20R ST", "C29 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C29/(C26-30)aaaSR"),
              #C30/(C26-30)aaaSR
                ratio_peaks(., c("C30 aaa 20R ST", "C30 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C30/(C26-30)aaaSR"),
           
              #C27/C27+C28aaa&abb
                ratio_peaks(., c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C27/C27+C28aaa&abb"),
              #C27/C27+C29aaa&abb
                ratio_peaks(., c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST")  , "C27/C27+C29aaa&abb"),
              #C28/C28+C27aaa&abb
                ratio_peaks(., c("C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C28/C28+C27aaa&abb"),
              #C28/C28+C29aaa&abb
                ratio_peaks(., c("C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST"), c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C28/C28+C29aaa&abb"),
              #C29/C29+C27aaa&abb
                ratio_peaks(., c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST")  , "C29/C29+C27aaa&abb"),
              #C29/C29+C28aaa&abb
                ratio_peaks(., c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST"), c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C29/C29+C28aaa&abb"),
              
              #4Me_TriMe/Me_C26St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C26 aBB 20S ST", "C26 aBB 20R ST", "C26 aaa 20S ST", "C26 aaa 20R ST") , "4Me_TriMe/Me_C26St"),
              #4Me_TriMe/Me_C27St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C27 aBB 20S ST", "C27 aBB 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST") , "4Me_TriMe/Me_C27St"),
              #4Me_TriMe/Me_C28St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST") , "4Me_TriMe/Me_C28St"),
              #4Me_TriMe/Me_C29St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST") , "4Me_TriMe/Me_C29St"),
              #4Me_TriMe/Me_C30St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C30 aBB 20 R+S ST", "C30 aaa 20S ST", "C30 aaa 20R ST") , "4Me_TriMe/Me_C30St"),
              #4Me_TriMe/Me_allSt
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "allRegst") , "4Me_TriMe/Me_allSt"),
           
              #C26-30St/C26-C30St+regHo 
                ratio_peaks(., c("allRegst"), c("allRegst", "Ts C27 HO", "Tm C27 HO", "C27 17B HO", "29, 30 C28 bisnor HO", "28, 30 C28 bisnor HO", "C29 Ts HO", "C29 Ba HO", "C29 BB Ho", "C30 aB HO", "C30 BB HO", "C30H Ba HO", "C31 HR Ba HO", "C31 aB HR HO", "C31 aB HS HO", "C31 BB HO", "C32 aB HS HO", "C32 aB HR HO", "C33 aB HS HO", "C33 aB HR HO", "C34 aB HR HO", "C34 aB HS HO", "C35 aB HR HO", "C35 aB HS HO"), "C26-30St/C26-C30St_regHo"),
              #C27-C30aaaSt/C27-C30aaaSt+regHo
                ratio_peaks(., c( "C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST", "allRegHO"), "C27-C30aaaSt/C27-C30aaaSt+regHo"),
              #Ho/St
                ratio_peaks(., "allRegHO", c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), "Ho/St"),
              #Ho/St%
                ratio_peaks(., "allRegHO", c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST", "allRegHO" ), "Ho/St%"),
            
              #C31_2MHI
                ratio_peaks(., "C31 2a Me Ho", c("C30 aB HO", "C31 2a Me Ho" ), "C31_2MHI"),
              #C31_35_2MHI
                ratio_peaks(., c("C31 2a Me Ho", "C32 2aMe R HO", "C32 2aMe S HO", "C33 2aMe S HO", "C33 2aMe R HO", "C34 2a Me S HO", "C34 2a Me R HO", "C36 2a Me R HO", "C36 2a Me S HO"), c("C30 aB HO", "C31 2a Me Ho", "C32 2aMe R HO", "C32 2aMe S HO", "C33 2aMe S HO", "C33 2aMe R HO", "C34 2a Me S HO", "C34 2a Me R HO", "C36 2a Me R HO", "C36 2a Me S HO"), "C31_35_2MHI"),
              #C31_2-MHI/C27-C30Steranes
                ratio_peaks(., "C31 2a Me Ho", c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST" ,"C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST", "C31 2a Me Ho" ), "C31_2-MHI/C27-C30Steranes"),
              #C31 3-MHI 
                ratio_peaks(., "C31 3B Me HO", c("C31 3B Me HO", "C30 aB HO"), "C31 3-MHI"), 
              #C31_35_3MHI(%)
                 ratio_peaks(., c("C31 3B Me HO", "C32 3B Me S HO", "C32 3B Me R HO", "C32 3B Me Ba 22S+R ST", "C33 3BMe S HO", "   
C33 3BMe R HO", "C34 3B Me S Ho", "C34 3B Me R HO", "C35 3B Me R HO", "C35 3B Me S HO", "C36 3B Me S HO", "C36 3B Me R HO"), c("C30 aB HO","C31 3B Me HO", "C32 3B Me S HO", "C32 3B Me R HO", "C32 3B Me Ba 22S+R ST", "C33 3BMe S HO", "C33 3BMe R HO", "C34 3B Me S HO", "C34 3B Me R HO", "C35 3B Me R HO", "C35 3B Me S HO", "C36 3B Me S HO", "C36 3B Me R HO" ) ,"C31_35_3MHI(%)"),

              #C29ab/C29ab+C30ab
                 ratio_peaks(., "C29 aB HO", c( "C29 aB HO" , "C30 aB HO"), "C29ab/C29ab+C30ab"), 
              #C29ab/allHoab
                 ratio_peaks(., "C29 aB HO" , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C29ab/allHoab"), 
              #C30ab/allHoab 
                 ratio_peaks(., "C30 aB HO" , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C30ab/allHoab"), 
              #C31ab/allHoab 
                 ratio_peaks(., c("C31 aB HS HO", "C31 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C31ab/allHoab"),
              #C32ab/allHoab 
                 ratio_peaks(., c("C32 aB HR HO", "C32 aB HS HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C32ab/allHoab"),
              #C33ab/allHoab 
                 ratio_peaks(., c( "C33 aB HS HO" , "C33 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C33ab/allHoab"),
              #C34ab/allHoab 
                 ratio_peaks(., c( "C34 aB HS HO", "C34 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C34ab/allHoab"),
              #C35ab/allHoab 
                 ratio_peaks(., c("C35 aB HS HO", "C35 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C35ab/allHoab"),
              #OleananeIndex
                ratio_peaks(., "Oleanane HO", c("Oleanane HO", "C30 aB HO"), "OleananeIndex"),

            #Source
              #HHI
                ratio_peaks(., c("C35 aB HS HO", "C35 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO"), "HHI"),
              #C35/C35+C34
                ratio_peaks(., c("C35 aB HS HO", "C35 aB HR HO"), c("C34 aB HS HO", "C34 aB HR HO","C35 aB HS HO", "C35 aB HR HO"), "C35/C35+C34"),
              #GI
                ratio_peaks(., "gamma", c("gamma", "C30 aB HO"), "GI"),
              #28,30BNH/28,30BNH+C30
                ratio_peaks(., "28, 30 C28 bisnor HO", c("28, 30 C28 bisnor HO", "C30 aB HO"), "28,30BNH/28,30BNH+C30")
              
 ) }) %>% ungroup() 
  
final_data

Against depth

D4

subset(final_data, peak_name=="D4 C29 ISTD") %>% 
    ggplot() +
    aes(x = amount.ug, y = depth) +
    geom_point() +
    facet_wrap(~peak_name, scales = "free") +
    scale_y_reverse() 
## Warning: Removed 16 rows containing missing values (geom_point).

ratios etc

subset(final_data, peak_name== "C27Dia/Reg") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Dia/Reg") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Dia_S/R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 19 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Reg_abb/aaa") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Regaaa_S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Regabb_S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28Dia/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28DiaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28abb/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28aaaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28abbS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29Dia/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29DiaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29abb/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29aaaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29abbS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Ts/Tm") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 22 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28BNH29,30/28,30") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 21 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29Ts/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29ba/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 16 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29bb/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30_30nor/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30ba/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 16 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30bb/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 16 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C32S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C33S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C34S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 19 rows containing missing values (geom_point).

subset(final_data, peak_name== "C35S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C19/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C20/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C21/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C22/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C23/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C24/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C25/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "tricyclics/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C19/C19+23") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 19 rows containing missing values (geom_point).

subset(final_data, peak_name== "C20/C20+23") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 18 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30Me/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "DinoSt/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27/C27+C28aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27/C27+C29aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28/C28+C27aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28/C28+C29aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29/C29+C27aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29/C29+C28aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C26St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C27St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C28St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C29St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C30St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26-30St/C26-C30St_regHo") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27-C30aaaSt/C27-C30aaaSt+regHo") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "Ho/St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_2MHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 16 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_35_2MHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_2-MHI/C27-C30Steranes") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31 3-MHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_35_3MHI(%)") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29ab/C29ab+C30ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C32ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C33ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C34ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C35ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "OleananeIndex") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "HHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "C35/C35+C34") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "GI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).

subset(final_data, peak_name== "28,30BNH/28,30BNH+C30") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()
## Warning: Removed 17 rows containing missing values (geom_point).